Search found 530 matches

by katharina
Wed Nov 18, 2015 6:39 pm
Forum: Training AUGUSTUS
Topic: augustus training and prediction from scratch
Replies: 3
Views: 2693

Re: augustus training and prediction from scratch

Originally posted by Cecilia in the old forum on 24.05.2012 - 02:36 Thanks Katharina. So my command will become: •autoAug.pl --species=NewSpecies --genome=genome.fa --pasa --cdna=evidence.fa I guess the pasa pipeline will handle the EST/transcript alignments to genome so I'm safe to skip the blat/h...
by katharina
Wed Nov 18, 2015 6:39 pm
Forum: Training AUGUSTUS
Topic: augustus training and prediction from scratch
Replies: 3
Views: 2693

Re: augustus training and prediction from scratch

Originally posted by katharina in the old forum on 23.05.2012 - 23:07 You shouldn't use the trainingset flag if you use cDNA-data. trainingset is used for protein sequences, genbank and gff training gene files, only. The value of maxIntronLen could be estimated if you inspect spliced alignments of ...
by katharina
Wed Nov 18, 2015 6:38 pm
Forum: Training AUGUSTUS
Topic: augustus training and prediction from scratch
Replies: 3
Views: 2693

augustus training and prediction from scratch

Originally posted by Cecilia in the old forum on 23.05.2012 - 21:59 I've got genome.fa, some EST sequences and RNA-Seq data for a species. How to do training and genome annotaion using augustus pipeline? My plan is * De novo assembly of RNA-seq reads and get transcripts.fasta file * cat transcripts...
by katharina
Wed Nov 18, 2015 6:37 pm
Forum: Predicting Genes with AUGUSTUS
Topic: X's in the predicted amino acid sequences
Replies: 1
Views: 1526

Re: X's in the predicted amino acid sequences

Originally posted by Mario in the old forum on 04.05.2012 - 12:16 They stem from n's in the genome assembly. On a hard-masked genome or when there are assembly gaps, the genome contains unknown nucleotides (N or n). These are by default considered to be somewhat less likely to be in coding regions,...
by katharina
Wed Nov 18, 2015 6:36 pm
Forum: Predicting Genes with AUGUSTUS
Topic: X's in the predicted amino acid sequences
Replies: 1
Views: 1526

X's in the predicted amino acid sequences

Originally posted by Sunghee in the old forum on 04.05.2012 - 12:11

In the output of Augustus I have X's in the amino acid sequences.
E.g. SADXXXXXXXXXXXGELD....
Would you tell me what it is?
by katharina
Wed Nov 18, 2015 6:35 pm
Forum: Predicting Genes with AUGUSTUS
Topic: very short introns
Replies: 3
Views: 2490

Re: very short introns

Originally posted by Mario in the old forum on 16.04.2012 - 13:50 Yes. In the text file tetrahymena_intron_probs.pbl or whatever it is called for your species edit the section after [LENGTH] which gives the intron length distribution. You can fill in a desired length distribution, e.g. with all zer...
by katharina
Wed Nov 18, 2015 6:35 pm
Forum: Predicting Genes with AUGUSTUS
Topic: very short introns
Replies: 3
Views: 2490

Re: very short introns

Originally posted by Olivier in the old forum on 16.04.2012 - 13:49

Is there a way to force augustus to put only introns with length < 100 nt? (like --max_intron_len=100 ?)
Thanks again
Best
Olivier
by katharina
Wed Nov 18, 2015 6:34 pm
Forum: Predicting Genes with AUGUSTUS
Topic: very short introns
Replies: 3
Views: 2490

Re: very short introns

Originally posted by Mario in the old forum on 11.04.2012 - 16:18 You can set the minimum intron length like this augustus --species=tetrahymena --min_intron_len=15 example.fa The default is 39bp, which for most species is a safe minimum. It makes sense to not decrease this below the actual minimum...
by katharina
Wed Nov 18, 2015 6:34 pm
Forum: Predicting Genes with AUGUSTUS
Topic: very short introns
Replies: 3
Views: 2490

very short introns

Originally posted by Olivier in the old forum on 11.04.2012 - 13:13 Hello, I am trying to use augustus to annotate our genome [...] Apparently you already have trained augustus with Tetrahymena, which is the closest model organism. I have ESTs and I have generated a hint file : scaffold51_5 EST51 e...
by katharina
Wed Nov 18, 2015 6:31 pm
Forum: Welcome to AUGUSTUS Forum!
Topic: Nettiquette
Replies: 0
Views: 3591

Nettiquette

Welcome to the AUGUSTUS Forum! The aim of this forum is to provide a discussion platform for all questions about gene prediction, in particular, about gene prediction with AUGUSTUS. Please adhere to the following rules: Respect: Treat other with respect, as you expect to be treated with respect, yo...